Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
jmjd-2

Cell type

Cell type Class
Larvae
Cell type
L3
NA
NA

Attributes by original data submitter

Sample

source_name
whole organism
strain
N2
developmental stage
L3
chip antibody
JMJD-2 (JA lab; Q3951)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Extract preparation and chromatin immunoprecipitation were performed as in Kolasinska-Zwierz et al. (2009) with the following modifications: tissue was fixed for 10 min in 1.5 mM EGS (Pierce 21565) then formaldehyde added to 1% for a further 10 min before quenching with 0.125M glycine and washing 2X with PBS plus protease inhibitors. Pellets were washed once in FA buffer, then resuspended in 1 ml FA buffer per 1 mL of ground worm powder and the extract sonicated to an average size of 250 base pairs with a Diagenode Bioruptor or Bioruptor Pico for 28 pulses of 30 s followed by 30 s pause. Following ChIP and DNA purification, libraries were prepared using the Illumina TruSeq kit. Fragments in the 250–300 base pair range were selected using Agencourt AMPure XP beads. Two biological replicate ChIPs were conducted for each factor.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

ce11

Number of total reads
15470898
Reads aligned (%)
94.8
Duplicates removed (%)
15.0
Number of peaks
6093 (qval < 1E-05)

ce10

Number of total reads
15470898
Reads aligned (%)
94.8
Duplicates removed (%)
15.0
Number of peaks
6089 (qval < 1E-05)

Base call quality data from DBCLS SRA